INTELLIGENT AUTOMATED RESTRICTION MAPPING TOOL

智能自动化限制图谱工具

• 批准号: 2209202
• 负责人: PETER C NELSON
• 金额: $ 13.41万
• 依托单位: UNIVERSITY OF ILLINOIS AT CHICAGO
• 依托单位国家: 美国
• 财政年份: 1993
• 资助国家: 美国
• 起止时间: 1993-12-10 至 1996-11-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2209202
• 关键词: artificial intelligence; automated data processing; computer program /software; computer simulation; computer system design /evaluation; genetic mapping; genetic markers; restriction fragment length polymorphism; restriction mapping

DESCRIPTION (Adapted from the Investigator's Abstract): Numerous restriction mapping programs have been devised since 1978, but none of them is as precise as manual map construction using digest gel photos, pencil, and graph paper. Given realistic data, programs usually find hundreds or even thousands of solutions, only one of which can be correct. Because of this, slow and demanding manual techniques are still in common use. The researchers propose to develop public domain software implementing a complete restriction mapping environment which will be far more powerful and useful than current restriction mapping software. This system will: 1) find solutions more quickly than any existing software; 2) find far fewer false maps than any existing software; 3) allow the user to "steer" the entire mapping process (if desired); and 4) guide the user with detailed, expert advice on handling specific mapping problems as they arise. In addition, the system will have: 5) built-in extensibility, so that simple modifications will also allow other genetic marker mapping problems to be solved by the same program and 6) the ability to record all user activity transparently, providing quantitative data on successful mapping strategies. The system will be based on extant restriction mapping programs, but it will overcome their limitations by including the following additional capabilities: 1) All known heuristics will be implemented. (Heuristics are logical rules of thumb which guide the search towards a true solution.) Existing programs use only a small subset of the known heuristics. Every added heuristic will speed up the search and reduce the set of possible solutions to a problem. 2) Hand mapping will be simulated on-screen via a "what you see is what you get" graphical user interface, with users choosing fully automatic mapping (the default), fully manual mapping (with simulated pencils and log paper), or various in-between levels of semi-automatic assisted mapping. This will allow users to control or adjust any part of the mapping process if they so desire. 3) An expert system (a program which can answer queries and make decisions by consulting a knowledge database) will guide users through the mapping process. It will assist the process of data acquisition, help the user solve difficulties, and tutor inexperienced users. Considerable preliminary design work has already taken place, so implementation can begin almost at once. Software will be developed and tested iteratively ("rapid prototyping") to assure end-user satisfaction. To insure portability at the source code level, the two major modules of the system (fragment length derivation and mapping) will be coded in C++ using Boochs' object-oriented design methodology, and the user interface will be designed using a portable interface-building tool that works on a variety of computing platforms (including DOS machines, and the Macintosh). The expert system will be implemented using CLIPS, a portable C-based public domain expert system shell.

描述（改编自研究者摘要）：大量 自1978年以来，限制性酶切图谱程序已经被设计出来，但没有一个 就像手工绘制地图一样精确， 和坐标纸 如果给出真实的数据，程序通常会找到数百或 甚至有成千上万的解决方案，其中只有一个是正确的。 因为 这种缓慢而苛刻的手工技术仍然普遍使用。 的 研究人员建议开发公共领域软件， 一个完整的限制性作图环境， 并且比目前的限制性酶切图谱软件有用。 该系统将： 1)比任何现有软件更快地找到解决方案; 2）找到更远的 比任何现有的软件更少的错误地图; 3）允许用户“引导” 整个映射过程（如果需要）;以及4）指导用户 详细的，专业的意见，处理具体的映射问题，因为他们 起来。 此外，该系统将具有：5）内置的可扩展性，因此 简单的修改也可以让其他遗传标记作图 问题要解决的同一个程序和6）的能力，以记录所有 透明的用户活动，提供有关成功的 映射策略。 该系统将基于现存的限制性酶切图谱程序，但它 将通过增加以下内容来克服其局限性 能力：1）将实施所有已知的化学品。 （启发式） 是指导寻找真正解决方案的逻辑经验法则。） 现有的程序只使用了一小部分已知的算法。 每 增加的启发式将加速搜索并减少可能的 解决问题的方法 2)手动映射将通过 “所见即所得”的图形用户界面， 选择全自动映射（默认），全手动映射（使用 模拟铅笔和日志纸），或各种中间水平的 半自动辅助绘图。 这将允许用户控制或 调整映射过程的任何部分，如果他们愿意的话。 3)专家 系统（一个程序，可以回答查询，并作出决定，通过咨询 知识数据库）将指导用户完成制图过程。 它 将协助数据采集过程，帮助用户解决 困难，并辅导没有经验的用户。 初步设计工作已经展开， 几乎可以立即开始执行。 将开发软件， 反复测试（“快速原型”），以确保最终用户的满意度。 为了确保源代码级别的可移植性， 系统（片段长度推导和映射）将用C++编码 使用Boochs的面向对象的设计方法， 将使用便携式界面构建工具进行设计， 各种计算平台（包括DOS机器和Macintosh）。 该专家系统将使用CLIPS实现，CLIPS是一个基于C语言的可移植的 公共领域专家系统外壳。